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| | ==First crystal structure of an endo-inulinase, from Aspergillus ficuum: structural analysis and comparison with other GH32 enzymes.== | | ==First crystal structure of an endo-inulinase, from Aspergillus ficuum: structural analysis and comparison with other GH32 enzymes.== |
| - | <StructureSection load='3rwk' size='340' side='right' caption='[[3rwk]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3rwk' size='340' side='right'caption='[[3rwk]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3rwk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_ficuum Aspergillus ficuum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RWK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RWK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3rwk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_ficuum Aspergillus ficuum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RWK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RWK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inulinase Inulinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.7 3.2.1.7] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rwk OCA], [http://pdbe.org/3rwk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rwk RCSB], [http://www.ebi.ac.uk/pdbsum/3rwk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rwk ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rwk OCA], [https://pdbe.org/3rwk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rwk RCSB], [https://www.ebi.ac.uk/pdbsum/3rwk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rwk ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/INU2_ASPFI INU2_ASPFI]] Endo-inulinase involved in utilization of the plant storage polymer inulin, consisting of fructooligosaccharides with a degree of polymerization (DP) value from 2 to 60.<ref>PMID:24251113</ref> | + | [https://www.uniprot.org/uniprot/INU2_ASPFI INU2_ASPFI] Endo-inulinase involved in utilization of the plant storage polymer inulin, consisting of fructooligosaccharides with a degree of polymerization (DP) value from 2 to 60.<ref>PMID:24251113</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Aspergillus ficuum]] | | [[Category: Aspergillus ficuum]] |
| - | [[Category: Inulinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Housen, I]] | + | [[Category: Housen I]] |
| - | [[Category: Mayard, A]] | + | [[Category: Mayard A]] |
| - | [[Category: Michaux, C]] | + | [[Category: Michaux C]] |
| - | [[Category: Pouyez, J]] | + | [[Category: Pouyez J]] |
| - | [[Category: Roussel, G]] | + | [[Category: Roussel G]] |
| - | [[Category: Vandamme, A M]] | + | [[Category: Vandamme AM]] |
| - | [[Category: Wouters, J]] | + | [[Category: Wouters J]] |
| - | [[Category: Catalytic mechanism]]
| + | |
| - | [[Category: Cytosol]]
| + | |
| - | [[Category: Endo-inulinase]]
| + | |
| - | [[Category: Glycosidase hydrolase family 32]]
| + | |
| - | [[Category: Glycoside hydrolase family 32]]
| + | |
| - | [[Category: Glycosylation]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
3rwk is a 1 chain structure with sequence from Aspergillus ficuum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.1Å |
| Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
INU2_ASPFI Endo-inulinase involved in utilization of the plant storage polymer inulin, consisting of fructooligosaccharides with a degree of polymerization (DP) value from 2 to 60.[1]
Publication Abstract from PubMed
Endo-inulinase is a member of glycosidase hydrolase family 32 (GH32) degrading fructans of the inulin type with an endo-cleavage mode and is an important class of industrial enzyme. In the present study, we report the first crystal structure of an endo-inulinase, INU2, from Aspergillus ficuum at 1.5 A. It was solved by molecular replacement with the structure of exo-inulinase as search model. The 3D structure presents a bimodular arrangement common to other GH32 enzymes: a N-terminal 5-fold beta-propeller catalytic domain with four beta-sheets and a C-terminal beta-sandwich domain organized in two beta-sheets with five beta-strands. The structural analysis and comparison with other GH32 enzymes reveal the presence of an extra pocket in the INU2 catalytic site, formed by two loops and the conserved motif W-M(I)-N-D(E)-P-N-G. This cavity would explain the endo-activity of the enzyme, the critical role of Trp40 and particularly the cleavage at the third unit of the inulin(-like) substrates. Crystal structure at 2.1 A of INU2 complexed with fructosyl molecules, experimental digestion data and molecular modelling studies support these hypotheses.
First crystal structure of an endo-inulinase, INU2, from Aspergillus ficuum: Discovery of an extra-pocket in the catalytic domain responsible for its endo-activity.,Pouyez J, Mayard A, Vandamme AM, Roussel G, Perpete EA, Wouters J, Housen I, Michaux C Biochimie. 2012 Jun 28. PMID:22750808[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Vandamme AM, Michaux C, Mayard A, Housen I. Asparagine 42 of the conserved endo-inulinase INU2 motif WMNDPN from Aspergillus ficuum plays a role in activity specificity. FEBS Open Bio. 2013 Nov 1;3:467-72. doi: 10.1016/j.fob.2013.10.009. eCollection, 2013. PMID:24251113 doi:http://dx.doi.org/10.1016/j.fob.2013.10.009
- ↑ Pouyez J, Mayard A, Vandamme AM, Roussel G, Perpete EA, Wouters J, Housen I, Michaux C. First crystal structure of an endo-inulinase, INU2, from Aspergillus ficuum: Discovery of an extra-pocket in the catalytic domain responsible for its endo-activity. Biochimie. 2012 Jun 28. PMID:22750808 doi:10.1016/j.biochi.2012.06.020
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